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-rw-r--r--Makefile.am6
-rw-r--r--Makefile.in53
-rw-r--r--src/index.c16
-rw-r--r--src/index.h1
-rw-r--r--src/templates.c326
-rw-r--r--src/templates.h33
6 files changed, 27 insertions, 408 deletions
diff --git a/Makefile.am b/Makefile.am
index 052b9e62..8719496a 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -41,7 +41,7 @@ src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c \
src/cell.c src/image.c src/peaks.c src/index.c \
src/filters.c src/diffraction.c src/detector.c \
src/sfac.c src/dirax.c src/mosflm.c \
- src/reflections.c src/templates.c src/symmetry.c \
+ src/reflections.c src/symmetry.c \
src/geometry.c src/thread-pool.c \
src/beam-parameters.c src/reflist.c
if HAVE_OPENCL
@@ -100,7 +100,7 @@ endif
src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c \
src/utils.c src/detector.c src/peaks.c src/image.c \
src/stream.c src/index.c src/dirax.c src/mosflm.c \
- src/templates.c src/geometry.c src/symmetry.c \
+ src/geometry.c src/symmetry.c \
src/thread-pool.c src/reflist.c
src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
@@ -117,7 +117,7 @@ EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
src/render.h src/hdfsee.h src/dirax.h src/mosflm.h src/peaks.h \
src/index.h src/filters.h src/diffraction-gpu.h src/cl-utils.h \
src/symmetry.h src/povray.h src/index-priv.h src/geometry.h \
- src/templates.h src/render_hkl.h src/stream.h src/thread-pool.h \
+ src/render_hkl.h src/stream.h src/thread-pool.h \
src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h \
src/reflist.h
diff --git a/Makefile.in b/Makefile.in
index 3e8f1851..50e4837c 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -144,10 +144,9 @@ src_hdfsee_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
am__src_indexamajig_SOURCES_DIST = src/indexamajig.c src/hdf5-file.c \
src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
src/filters.c src/diffraction.c src/detector.c src/sfac.c \
- src/dirax.c src/mosflm.c src/reflections.c src/templates.c \
- src/symmetry.c src/geometry.c src/thread-pool.c \
- src/beam-parameters.c src/reflist.c src/diffraction-gpu.c \
- src/cl-utils.c
+ src/dirax.c src/mosflm.c src/reflections.c src/symmetry.c \
+ src/geometry.c src/thread-pool.c src/beam-parameters.c \
+ src/reflist.c src/diffraction-gpu.c src/cl-utils.c
@HAVE_OPENCL_TRUE@am__objects_1 = src/diffraction-gpu.$(OBJEXT) \
@HAVE_OPENCL_TRUE@ src/cl-utils.$(OBJEXT)
am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
@@ -156,10 +155,9 @@ am_src_indexamajig_OBJECTS = src/indexamajig.$(OBJEXT) \
src/filters.$(OBJEXT) src/diffraction.$(OBJEXT) \
src/detector.$(OBJEXT) src/sfac.$(OBJEXT) src/dirax.$(OBJEXT) \
src/mosflm.$(OBJEXT) src/reflections.$(OBJEXT) \
- src/templates.$(OBJEXT) src/symmetry.$(OBJEXT) \
- src/geometry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
- src/beam-parameters.$(OBJEXT) src/reflist.$(OBJEXT) \
- $(am__objects_1)
+ src/symmetry.$(OBJEXT) src/geometry.$(OBJEXT) \
+ src/thread-pool.$(OBJEXT) src/beam-parameters.$(OBJEXT) \
+ src/reflist.$(OBJEXT) $(am__objects_1)
src_indexamajig_OBJECTS = $(am_src_indexamajig_OBJECTS)
src_indexamajig_LDADD = $(LDADD)
src_indexamajig_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -208,9 +206,9 @@ am_src_reintegrate_OBJECTS = src/reintegrate.$(OBJEXT) \
src/cell.$(OBJEXT) src/hdf5-file.$(OBJEXT) src/utils.$(OBJEXT) \
src/detector.$(OBJEXT) src/peaks.$(OBJEXT) src/image.$(OBJEXT) \
src/stream.$(OBJEXT) src/index.$(OBJEXT) src/dirax.$(OBJEXT) \
- src/mosflm.$(OBJEXT) src/templates.$(OBJEXT) \
- src/geometry.$(OBJEXT) src/symmetry.$(OBJEXT) \
- src/thread-pool.$(OBJEXT) src/reflist.$(OBJEXT)
+ src/mosflm.$(OBJEXT) src/geometry.$(OBJEXT) \
+ src/symmetry.$(OBJEXT) src/thread-pool.$(OBJEXT) \
+ src/reflist.$(OBJEXT)
src_reintegrate_OBJECTS = $(am_src_reintegrate_OBJECTS)
src_reintegrate_LDADD = $(LDADD)
src_reintegrate_DEPENDENCIES = $(top_builddir)/lib/libgnu.a
@@ -555,17 +553,16 @@ EXTRA_DIST = configure m4/gnulib-cache.m4 src/cell.h src/hdf5-file.h \
src/dw-hdfsee.h src/render.h src/hdfsee.h src/dirax.h \
src/mosflm.h src/peaks.h src/index.h src/filters.h \
src/diffraction-gpu.h src/cl-utils.h src/symmetry.h \
- src/povray.h src/index-priv.h src/geometry.h src/templates.h \
- src/render_hkl.h src/stream.h src/thread-pool.h \
- src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h \
- src/reflist.h data/sfac/Ca.nff data/sfac/C.nff \
- data/sfac/Fe.nff data/sfac/H.nff data/sfac/Mg.nff \
- data/sfac/N.nff data/sfac/O.nff data/sfac/P.nff \
- data/sfac/S.nff data/sfac/f0_WaasKirf.dat data/defs.h \
- data/diffraction.cl data/hdfsee.ui doc/geometry.txt \
- doc/indexamajig.txt doc/pattern_sim.txt doc/process_hkl.txt \
- doc/symmetry.txt doc/twin-calculator.pdf doc/0-INDEX \
- doc/examples/lcls-dec.geom \
+ src/povray.h src/index-priv.h src/geometry.h src/render_hkl.h \
+ src/stream.h src/thread-pool.h src/beam-parameters.h \
+ src/post-refinement.h src/hrs-scaling.h src/reflist.h \
+ data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
+ data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff \
+ data/sfac/O.nff data/sfac/P.nff data/sfac/S.nff \
+ data/sfac/f0_WaasKirf.dat data/defs.h data/diffraction.cl \
+ data/hdfsee.ui doc/geometry.txt doc/indexamajig.txt \
+ doc/pattern_sim.txt doc/process_hkl.txt doc/symmetry.txt \
+ doc/twin-calculator.pdf doc/0-INDEX doc/examples/lcls-dec.geom \
doc/examples/lcls-june-r0013-r0128.geom \
doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom \
doc/examples/lcls-dec.beam doc/examples/lcls-june.beam \
@@ -597,9 +594,9 @@ src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c \
src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c \
src/utils.c src/cell.c src/image.c src/peaks.c src/index.c \
src/filters.c src/diffraction.c src/detector.c src/sfac.c \
- src/dirax.c src/mosflm.c src/reflections.c src/templates.c \
- src/symmetry.c src/geometry.c src/thread-pool.c \
- src/beam-parameters.c src/reflist.c $(am__append_4)
+ src/dirax.c src/mosflm.c src/reflections.c src/symmetry.c \
+ src/geometry.c src/thread-pool.c src/beam-parameters.c \
+ src/reflist.c $(am__append_4)
@HAVE_GTK_TRUE@src_hdfsee_SOURCES = src/hdfsee.c src/dw-hdfsee.c src/render.c \
@HAVE_GTK_TRUE@ src/hdf5-file.c src/utils.c src/image.c src/filters.c \
@HAVE_GTK_TRUE@ src/thread-pool.c src/detector.c
@@ -647,7 +644,7 @@ src_partialator_SOURCES = src/partialator.c src/cell.c src/hdf5-file.c \
src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c \
src/utils.c src/detector.c src/peaks.c src/image.c \
src/stream.c src/index.c src/dirax.c src/mosflm.c \
- src/templates.c src/geometry.c src/symmetry.c \
+ src/geometry.c src/symmetry.c \
src/thread-pool.c src/reflist.c
src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
@@ -860,8 +857,6 @@ src/diffraction.$(OBJEXT): src/$(am__dirstamp) \
src/dirax.$(OBJEXT): src/$(am__dirstamp) src/$(DEPDIR)/$(am__dirstamp)
src/mosflm.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
-src/templates.$(OBJEXT): src/$(am__dirstamp) \
- src/$(DEPDIR)/$(am__dirstamp)
src/geometry.$(OBJEXT): src/$(am__dirstamp) \
src/$(DEPDIR)/$(am__dirstamp)
src/reflist.$(OBJEXT): src/$(am__dirstamp) \
@@ -968,7 +963,6 @@ mostlyclean-compile:
-rm -f src/stream.$(OBJEXT)
-rm -f src/sum_stack.$(OBJEXT)
-rm -f src/symmetry.$(OBJEXT)
- -rm -f src/templates.$(OBJEXT)
-rm -f src/thread-pool.$(OBJEXT)
-rm -f src/utils.$(OBJEXT)
-rm -f tests/list_check.$(OBJEXT)
@@ -1016,7 +1010,6 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/stream.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/sum_stack.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/symmetry.Po@am__quote@
-@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/templates.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/thread-pool.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@src/$(DEPDIR)/utils.Po@am__quote@
@AMDEP_TRUE@@am__include@ @am__quote@tests/$(DEPDIR)/list_check.Po@am__quote@
diff --git a/src/index.c b/src/index.c
index 3d2246bc..d6375834 100644
--- a/src/index.c
+++ b/src/index.c
@@ -30,7 +30,6 @@
#include "detector.h"
#include "index.h"
#include "index-priv.h"
-#include "templates.h"
/* Base class constructor for unspecialised indexing private data */
@@ -67,10 +66,6 @@ IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
case INDEXING_MOSFLM :
iprivs[n] = indexing_private(indm[n]);
break;
- case INDEXING_TEMPLATE :
- iprivs[n] = generate_templates(cell, filename, det,
- nominal_photon_energy);
- break;
}
}
@@ -98,8 +93,6 @@ void cleanup_indexing(IndexingPrivate **priv)
case INDEXING_MOSFLM :
free(priv[n]);
break;
- case INDEXING_TEMPLATE :
- free_templates(priv[n]);
}
n++;
@@ -153,18 +146,14 @@ void index_pattern(struct image *image, UnitCell *cell, IndexingMethod *indm,
STATUS("Running MOSFLM...\n");
run_mosflm(image, cell);
break;
- case INDEXING_TEMPLATE :
- match_templates(image, ipriv[n]);
- break;
}
-
if ( image->ncells == 0 ) {
STATUS("No candidate cells found.\n");
n++;
continue;
}
- if ( (cellr == CELLR_NONE) || (indm[n] == INDEXING_TEMPLATE) ) {
+ if ( cellr == CELLR_NONE ) {
image->indexed_cell = cell_new_from_cell(
image->candidate_cells[0]);
if ( verbose ) {
@@ -254,9 +243,6 @@ IndexingMethod *build_indexer_list(const char *str, int *need_cell)
list[i] = INDEXING_DIRAX;
} else if ( strcmp(methods[i], "mosflm") == 0) {
list[i] = INDEXING_MOSFLM;
- } else if ( strcmp(methods[i], "template") == 0) {
- list[i] = INDEXING_TEMPLATE;
- *need_cell = 1;
} else {
ERROR("Unrecognised indexing method '%s'\n",
methods[i]);
diff --git a/src/index.h b/src/index.h
index 8f3e0ab7..005f0d93 100644
--- a/src/index.h
+++ b/src/index.h
@@ -28,7 +28,6 @@ typedef enum {
INDEXING_NONE,
INDEXING_DIRAX,
INDEXING_MOSFLM,
- INDEXING_TEMPLATE
} IndexingMethod;
diff --git a/src/templates.c b/src/templates.c
deleted file mode 100644
index ed557afa..00000000
--- a/src/templates.c
+++ /dev/null
@@ -1,326 +0,0 @@
-/*
- * templates.c
- *
- * Indexing by template matching
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "index.h"
-#include "index-priv.h"
-#include "symmetry.h"
-#include "utils.h"
-#include "geometry.h"
-#include "hdf5-file.h"
-#include "peaks.h"
-#include "reflist.h"
-
-#include <assert.h>
-
-
-#define INTEGRATION_SQUARE_SIDE (10)
-#define THRESHOLD (500)
-
-
-/* Private data for template indexing */
-struct _indexingprivate_template
-{
- struct _indexingprivate base;
- UnitCell *cell;
- int n_templates;
- struct template *templates;
-};
-
-
-struct template {
- double omega;
- double phi;
- RefList *spots;
-};
-
-
-/* Generate templates for the given cell using a representative image */
-IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
- struct detector *det,
- double nominal_photon_energy)
-{
- struct _indexingprivate_template *priv;
- const char *sym;
- double omega_max, phi_max;
- int n_templates;
- const double omega_step = deg2rad(0.5);
- const double phi_step = deg2rad(0.5);
- double omega, phi;
- struct image image;
- struct hdfile *hdfile;
- int i;
-
- hdfile = hdfile_open(filename);
- if ( hdfile == NULL ) {
- return NULL;
- } else if ( hdfile_set_image(hdfile, "/data/data0") ) {
- ERROR("Couldn't select path\n");
- return NULL;
- }
- hdf5_read(hdfile, &image, 0);
- hdfile_close(hdfile);
- image.det = det;
- if ( image.lambda < 0.0 ) image.lambda = nominal_photon_energy;
-
- priv = calloc(1, sizeof(struct _indexingprivate_template));
- priv->base.indm = INDEXING_TEMPLATE;
-
- sym = cell_get_pointgroup(cell);
-
- /* These define the orientation in space */
- if ( is_polyhedral(sym) ) {
- ERROR("WARNING: Point group is polyhedral.\n");
- ERROR("This means I can't properly determine the orientation");
- ERROR(" ranges for template matching. Expect trouble.\n");
- }
- omega_max = 2.0*M_PI / rotational_order(sym);
- if ( has_bisecting_mirror_or_diad(sym) ) omega_max /= 2.0;
- phi_max = M_PI;
- if ( has_perpendicular_mirror(sym) ) phi_max /= 2.0;
-
- /* One more axis would define the rotation in the plane of the image */
-
- STATUS("Orientation ranges in %s: %.0f-%.0f, %.0f-%.0f deg.\n",
- sym, 0.0, rad2deg(omega_max), 0.0, rad2deg(phi_max));
-
- n_templates = (omega_max * phi_max)/(omega_step * phi_step);
- STATUS("%i templates to be calculated.\n", n_templates);
-
- priv->templates = malloc(n_templates * sizeof(struct template));
-
- i = 0;
- for ( omega = 0.0; omega < omega_max-omega_step; omega += omega_step ) {
- for ( phi = 0.0; phi < phi_max-phi_step; phi += phi_step ) {
-
- RefList *reflections;
- UnitCell *cell_rot;
-
- assert(i < n_templates);
-
- cell_rot = rotate_cell(cell, omega, phi, 0.0);
-
- reflections = find_intersections(&image, cell_rot, 0);
- if ( reflections == NULL ) {
- ERROR("Template calculation failed.\n");
- return NULL;
- }
-
- priv->templates[i].omega = omega;
- priv->templates[i].phi = phi;
- priv->templates[i].spots = reflections;
- i++;
-
- free(cell_rot);
-
- }
- progress_bar(omega*1000.0, (omega_max-2.0*omega_step)*1000.0,
- "Generating templates");
- }
-
- priv->n_templates = n_templates;
- priv->cell = cell_new_from_cell(cell);
-
- free(image.data);
- free(image.flags);
-
- return (struct _indexingprivate *)priv;
-}
-
-
-static int fast_integrate_peak(struct image *image, int xp, int yp)
-{
- int x, y;
- double total = 0;
- int r = INTEGRATION_SQUARE_SIDE;
-
- for ( x=xp-r; x<=xp+r; x++ ) {
- for ( y=yp-r; y<=yp+r; y++ ) {
-
- int val;
-
- if ( (x>=image->width) || (x<0) ) continue;
- if ( (y>=image->height) || (y<0) ) continue;
-
- val = image->data[x+image->width*y];
-
- if ( val < THRESHOLD ) continue;
- total += val;
-
- }
- }
-
- return total;
-}
-
-
-static double integrate_all_rot(struct image *image, RefList *reflections,
- double rot)
-{
- double itot = 0.0;
- double cosr, sinr;
- int num_int = 0;
- Reflection *refl;
- RefListIterator *iter;
-
- cosr = cos(rot);
- sinr = sin(rot);
-
- for ( refl = first_refl(reflections, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) ) {
-
- float xp, yp;
- double x, y;
-
- get_detector_pos(refl, &x, &y);
-
- xp = cosr*x + sinr*y;
- yp = -sinr*x + cosr*y;
-
- itot += fast_integrate_peak(image, rint(xp), rint(yp));
- num_int++;
-
- }
-
- return itot / num_int;
-}
-
-
-/* Return the mean of the distances between peaks in the image and peaks from
- * the given template. */
-static double mean_distance(struct image *image, RefList *reflections,
- double rot)
-{
- double dtot = 0.0;
- double cosr, sinr;
- int num_dist = 0;
- Reflection *refl;
- RefListIterator *iter;
-
- cosr = cos(rot);
- sinr = sin(rot);
-
- /* For each template peak */
- for ( refl = first_refl(reflections, &iter);
- refl != NULL;
- refl = next_refl(refl, iter) ) {
-
- float xp, yp;
- int j;
- double min_dsq;
- double x, y;
-
- get_detector_pos(refl, &x, &y);
-
- xp = cosr*x + sinr*y;
- yp = -sinr*x + cosr*y;
-
- /* Compare to every real peak */
- min_dsq = +INFINITY;
- for ( j=0; j<image_feature_count(image->features); j++ ) {
-
- struct imagefeature *f;
- double this_dsq;
-
- f = image_get_feature(image->features, j);
-
- this_dsq = pow(f->x - xp, 2.0) + pow(f->y - yp, 2.0);
- if ( this_dsq < min_dsq ) min_dsq = this_dsq;
-
- }
-
- if ( min_dsq < pow(50.0, 2.0) ) {
- dtot += sqrt(min_dsq);
- num_dist++;
- }
-
- }
-
- return dtot / num_dist;
-}
-
-
-void match_templates(struct image *image, IndexingPrivate *ipriv)
-{
- struct _indexingprivate_template *priv
- = (struct _indexingprivate_template *)ipriv;
- int i, max_i;
- double max, rot, rot_max, rot_step, rot_best;
- const int peaks = 0;
-
- if ( peaks ) {
- max = INFINITY;
- } else {
- max = 0.0;
- }
- max_i = 0;
- rot_max = 2.0*M_PI;
- rot_step = 2.0*M_PI / 360.0; /* 1 deg steps */
- rot_best = 0.0;
-
- for ( i=0; i<priv->n_templates; i++ ) {
- for ( rot=0.0; rot<rot_max; rot+=rot_step ) {
-
- double val;
- int best;
-
- if ( !peaks ) {
- val = integrate_all_rot(image, priv->templates[i].spots,
- rot);
- best = val > max;
- } else {
- val = mean_distance(image, priv->templates[i].spots,
- rot);
- best = val < max;
- }
-
- if ( best ) {
- max = val;
- max_i = i;
- rot_best = rot;
- }
-
- }
- progress_bar(i, priv->n_templates-1, "Indexing");
- }
-
- STATUS("%i (%.2f, %.2f, %.2f): %.2f\n", max_i,
- rad2deg(priv->templates[max_i].omega),
- rad2deg(priv->templates[max_i].phi),
- rad2deg(rot_best), max);
-
- image->ncells = 1;
- image->candidate_cells[0] = rotate_cell(priv->cell,
- priv->templates[max_i].omega,
- priv->templates[max_i].phi,
- rot_best);
-}
-
-
-void free_templates(IndexingPrivate *priv)
-{
- int i;
- struct _indexingprivate_template *tpriv
- = (struct _indexingprivate_template *)priv;
-
- for ( i=0; i<tpriv->n_templates; i++ ) {
- free(tpriv->templates[i].spots);
- }
-
- free(tpriv->templates);
- cell_free(tpriv->cell);
- free(tpriv);
-}
diff --git a/src/templates.h b/src/templates.h
deleted file mode 100644
index 33e6c75e..00000000
--- a/src/templates.h
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * templates.h
- *
- * Indexing by template matching
- *
- * (c) 2006-2010 Thomas White <taw@physics.org>
- *
- * Part of CrystFEL - crystallography with a FEL
- *
- */
-
-#ifndef TEMPLATES_H
-#define TEMPLATES_H
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-
-#include "index.h"
-#include "image.h"
-#include "cell.h"
-
-extern IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
- struct detector *det,
- double nominal_photon_energy);
-
-
-extern void match_templates(struct image *image, IndexingPrivate *ipriv);
-
-extern void free_templates(IndexingPrivate *priv);
-
-#endif /* TEMPLATES_H */
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-10 12:52:39 +0000